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PDBsum entry 3b82

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protein ligands Protein-protein interface(s) links
Biosynthetic protein/transferase PDB id
3b82
Jmol
Contents
Protein chains
823 a.a. *
207 a.a. *
Ligands
NAD ×3
Waters ×548
* Residue conservation analysis
PDB id:
3b82
Name: Biosynthetic protein/transferase
Title: Structure of the eef2-exoa(e546h)-NAD+ complex
Structure: Elongation factor 2. Chain: a, c, e. Synonym: ef-2, translation elongation factor 2, eukaryotic elongation factor 2, eef2, ribosomal translocase. Exotoxin a. Chain: b, d, f. Fragment: catalytic domain. Synonym: NAD-dependent adp-ribosyltransferase. Engineered: yes.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Pseudomonas aeruginosa. Organism_taxid: 287. Gene: eta. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.35Å     R-factor:   0.215     R-free:   0.257
Authors: R.Jorgensen,A.R.Merrill
Key ref: R.Jørgensen et al. (2008). The nature and character of the transition state for the ADP-ribosyltransferase reaction. EMBO Rep, 9, 802-809. PubMed id: 18583986
Date:
31-Oct-07     Release date:   17-Jun-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P32324  (EF2_YEAST) -  Elongation factor 2
Seq:
Struc:
 
Seq:
Struc:
842 a.a.
823 a.a.*
Protein chains
Pfam   ArchSchema ?
P11439  (TOXA_PSEAE) -  Exotoxin A
Seq:
Struc:
 
Seq:
Struc:
638 a.a.
207 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains B, D, F: E.C.2.4.2.36  - NAD(+)--diphthamide ADP-ribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
NAD(+)
+ diphthamide-[translation elongation factor 2]
= nicotinamide
+ N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    Added reference    
 
 
EMBO Rep 9:802-809 (2008)
PubMed id: 18583986  
 
 
The nature and character of the transition state for the ADP-ribosyltransferase reaction.
R.Jørgensen, Y.Wang, D.Visschedyk, A.R.Merrill.
 
  ABSTRACT  
 
Exotoxin A (ExoA) from Pseudomonas aeruginosa is an important virulence factor that belongs to a class of exotoxins that are secreted by pathogenic bacteria which cause human diseases such as cholera, diphtheria, pneumonia and whooping cough. We present the first crystal structures, to our knowledge, of ExoA in complex with elongation factor 2 (eEF2) and intact NAD(+), which indicate a direct role of two active-site loops in ExoA during the catalytic cycle. One loop moves to form a solvent cover for the active site of the enzyme and reaches towards the target residue (diphthamide) in eEF2 forming an important hydrogen bond. The NAD(+) substrate adopts a conformation remarkably different from that of the NAD(+) analogue, betaTAD, observed in previous structures, and fails to trigger any loop movements. Mutational studies of the two loops in the toxin identify several residues important for catalytic activity, in particular Glu 546 and Arg 551, clearly supporting the new complex structures. On the basis of these data, we propose a transition-state model for the toxin-catalysed reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20106667 M.O.Hottiger, P.O.Hassa, B.Lüscher, H.Schüler, and F.Koch-Nolte (2010).
Toward a unified nomenclature for mammalian ADP-ribosyltransferases.
  Trends Biochem Sci, 35, 208-219.  
21170356 R.J.Fieldhouse, Z.Turgeon, D.White, and A.R.Merrill (2010).
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases.
  PLoS Comput Biol, 6, e1001029.  
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